debian/changelog

 sailfish (0.10.1+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #nnnn)
+  
+  TODO:
+    1. Code relies on old version of spdlog since it tries to include
+       spdlog/details/format.h
+       I've searched spdlog upstream Git.  This file was removed in
+    
+	commit f5bde237dda771f41e876ef7c7affc51db9c58f6 (HEAD)
+	Author: gabime <gmelman1@gmail.com>
+	Date:   Fri Jul 15 18:35:43 2016 +0300
+	
+	    Updated fmt lib to version 0d5ef5c2a66026409b0cfbafa1d2f46cdc5aa4d0
+
 
  -- Steffen Moeller <moeller@debian.org>  Thu, 21 Mar 2019 22:47:18 +0100

debian/patches/dfsg-please.patch

@@ -4,15 +4,28 @@ Description: Make sure we build against Debian packaged libraries
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -287,6 +287,7 @@ ExternalProject_Add(libdivsufsort
- set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+@@ -272,6 +272,7 @@ message("BOOST LIBRAREIS = ${Boost_LIBRA
+ 
+ set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
  
++if(!DEBIAN_BUILD)
+ message("Build system will build libdivsufsort")
+ message("==================================================================")
+ include(ExternalProject)
+@@ -285,8 +286,11 @@ ExternalProject_Add(libdivsufsort
+     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
+     )
+ set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
++else()
++message("Use Debian packaged libdivsufsort")
++endif()
  
+-
 +if(!DEBIAN_BUILD)
  message("Build system will fetch and build Jellyfish")
  message("==================================================================")
  ExternalProject_Add(libjellyfish
-@@ -303,6 +304,9 @@ ExternalProject_Add(libjellyfish
+@@ -303,6 +307,9 @@ ExternalProject_Add(libjellyfish
                      cp config.h <INSTALL_DIR>/include/jellyfish-2.2.3/jellyfish/ &&
                      cp config.h <INSTALL_DIR>/include/
  )
@@ -22,7 +35,7 @@ Description: Make sure we build against Debian packaged libraries
  
  find_package(TBB)
  ##
-@@ -311,6 +315,7 @@ find_package(TBB)
+@@ -311,6 +318,7 @@ find_package(TBB)
  #
  ##
  if(NOT TBB_FOUND)
@@ -30,7 +43,7 @@ Description: Make sure we build against Debian packaged libraries
  
  set(TBB_WILL_RECONFIGURE TRUE)
  # Set the appropriate compiler
-@@ -352,6 +357,9 @@ ExternalProject_Add_Step(libtbb reconfig
+@@ -352,6 +360,9 @@ ExternalProject_Add_Step(libtbb reconfig
          DEPENDEES install
  )
  endif()
@@ -40,7 +53,7 @@ Description: Make sure we build against Debian packaged libraries
  
  ## 
  #  Find HDF5, and prefer the static libs
-@@ -401,7 +409,7 @@ endif()
+@@ -401,7 +412,7 @@ endif()
  
  
  message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
@@ -49,7 +62,7 @@ Description: Make sure we build against Debian packaged libraries
  message("Build system will compile libgff")
  message("==================================================================")
  ExternalProject_Add(libgff
-@@ -416,6 +424,9 @@ ExternalProject_Add(libgff
+@@ -416,6 +427,9 @@ ExternalProject_Add(libgff
      BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
  )
@@ -59,7 +72,7 @@ Description: Make sure we build against Debian packaged libraries
  
  set (FAST_MALLOC_LIB "")
  set (HAVE_FAST_MALLOC FALSE)
-@@ -441,6 +452,8 @@ endif()
+@@ -441,6 +455,8 @@ endif()
  
  if (NOT HAVE_FAST_MALLOC)
      message("Build system will fetch and use JEMalloc")
@@ -68,7 +81,7 @@ Description: Make sure we build against Debian packaged libraries
      message("==================================================================")
      ExternalProject_Add(libjemalloc
          DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-@@ -456,10 +469,12 @@ if (NOT HAVE_FAST_MALLOC)
+@@ -456,10 +472,12 @@ if (NOT HAVE_FAST_MALLOC)
      set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
      set (HAVE_FAST_MALLOC TRUE)
  endif ()
@@ -81,7 +94,7 @@ Description: Make sure we build against Debian packaged libraries
  message("Build system will fetch and build SparseHash")
  message("==================================================================")
  ExternalProject_Add(libsparsehash
-@@ -472,6 +487,7 @@ ExternalProject_Add(libsparsehash
+@@ -472,6 +490,7 @@ ExternalProject_Add(libsparsehash
      CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
      INSTALL_COMMAND make install
  )

debian/upstream/metadata

@@ -2,7 +2,7 @@ Reference:
   Author: Rob Patro and Stephen M Mount and Carl Kingsford
   Title: >
    Sailfish enables alignment-free isoform quantification from RNA-seq reads
-   using lightweight algorithms"
+   using lightweight algorithms
   Journal: Nature Biotechnology
   Year: 2014
   Volume: 32